Storage optimization

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Revision as of 17:08, 5 October 2024 by Denperidge (talk | contribs) (Moving the store: fixed rsync --hard-links argument, merged rsync commands. Moved mount instructions from mounting on /mnt to mounting on /mnt/nix, added mount options)
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A recurring problem with NixOS is lack of space on /. Even if you only occasionally use Nix, it is easy for /nix/store to grow beyond reasonable sizes. What follows are generic notes on how to reduce the growth of the Nix store.

Optimising the store

Here, we demonstrate how to configure nix to save space via hardlinking store files.

Automatic

To turn on periodic optimisation of the nix store, set the following option in /etc/nixos/configuration.nix: 

configuration.nix

nix.optimise.automatic = true;
nix.optimise.dates = [ "03:45" ]; # Optional; allows customizing optimisation schedule

Alternatively, the store can be optimised during every build. This may slow down builds, as discussed here. To enable this behavior, set the following option: 

configuration.nix

nix.settings.auto-optimise-store = true;

Manual

Run # nix-store --optimise. This is a potentially long operation.

Garbage collection

The Nix store accumulates entries which are no longer useful.[cf. 1] They can be deleted with nix-collect-garbage [cf. 2] or nix-store --gc.[cf. 3]

Note that if a result file still exists in the file system, and your Nix configuration has both keep-outputs = true and keep-derivations = true, all the dependencies used to build it will be kept. To see which result files prevent garbage collection, run: 

$ nix-store --gc --print-roots
/home/danbst/dev/test-shell/.shell.drv -> /nix/store/4diqwczyjipdqyi7aj34wfagblbhfjr9-nixops-1.4
/home/danbst/dev/test-shell/.shell.drv-2 -> /nix/store/62h3c4d6rdnlxichixqg8h9jxi8nhxk0-stdenv
/home/danbst/dev/test-shell/.shell.drv-2-doc -> /nix/store/14gnv1q1w0n9qwa3q23idsqvn51354y8-bash-4.3-p42-doc
/home/danbst/stack/new/website/server/result -> /nix/store/1jhmp6vl364p32r8bjigk65qh1xa562f-server-0.1.0.0
/home/danbst/testing/.nix-gc-roots/shell.drv -> /nix/store/v3vqf48awjjzjivrx15kfqdh1d7cg4mq-sshpass-1.05
...
/home/danbst/testing/.nix-gc-roots/shell.drv-12 -> /nix/store/a2li4sl9pxh9aflqia2gp7w88ayvjwci-bash-4.3-p42
/home/danbst/testing/.nix-gc-roots/shell.drv-12-doc -> /nix/store/kcswyb1d8zimkym0pjfi2fj1dly1w34w-bash-4.3-p42-doc
/home/danbst/testing/.nix-gc-roots/shell.drv-12-info -> /nix/store/njb817fwiafswzwvj9skw7w7k6b3fnbi-bash-4.3-p42-info
/home/ec2-user/result -> /nix/store/q35aq2sh5dbyka6g6f6qb7b8msxwds5m-nixos-system-iron-16.03.1299.a8e0739
/nix/var/nix/profiles/per-container/analyt/system-3-link -> /nix/store/snrj72189wh9va23fawl3v80v92xnxlm-nixos-system-iron-16.03.1291.efe2d64
/nix/var/nix/profiles/per-container/d-live/system-6-link -> /nix/store/cp2c58hnczsjk5h69ksajq5xfhsyhl6v-nixos-system-iron-16.03.1299.a8e0739
/nix/var/nix/profiles/per-container/d-test/system-4-link -> /nix/store/n1w7ywjg65x8iimchznxcyygbgmyfh55-nixos-system-iron-16.03.1287.6ac7ffd
/nix/var/nix/profiles/per-container/dashboard/system-41-link -> /nix/store/7qk19pkwgq0h3a1q9dcql3nks40rr75s-nixos-system-iron-16.03.1340.5a090dd
...
/nix/var/nix/profiles/per-container/ttt/system-1-link -> /nix/store/1kj9qs5gl3421jlkl3jfc2kqdsl8akwr-nixos-system-ttt-16.03.977.1da05df
/nix/var/nix/profiles/per-user/danbst/channels-1-link -> /nix/store/s0qay9qyqrn92zayldbvvj3zrfcl7a72-user-environment
/nix/var/nix/profiles/per-user/danbst/profile-28-link -> /nix/store/69ds606146dqml04sm0fbpqwnv2w8i3q-user-environment
/nix/var/nix/profiles/per-user/ec2-user/profile-7-link -> /nix/store/y2hc7zsnkzys9ba6xaijvjhff03rcgpy-user-environment
/nix/var/nix/profiles/per-user/root/channels-4-link -> /nix/store/254b6pkhhnjywvj5c0lp2vdai8nz4p0g-user-environment
/nix/var/nix/profiles/system-398-link -> /nix/store/wmndyzzrbc9fyjw844jmvzwgwgcinq7s-nixos-system-iron-16.0916.09pre.custom
/root/forkstat/result -> /nix/store/i5glmg3wk2a48x52rhd92zip1cmc0kq9-forkstat-git
/run/booted-system -> /nix/store/8jkrl9jyq7hqxb6xpwcaghpdm26gq98j-nixos-system-iron-16.0916.09pre.custom
/run/current-system -> /nix/store/wmndyzzrbc9fyjw844jmvzwgwgcinq7s-nixos-system-iron-16.0916.09pre.custom

GC roots can be found in /nix/var/nix/gcroots. The following script demonstrates how this directory can be used to (for example) query the state of manually made result symlinks: 

$ find -H /nix/var/nix/gcroots/auto -type l | xargs -I {} sh -c 'readlink {}; realpath {}; echo'

This acts a simpler (but faster) version of --print-roots and could be implemented as a bash alias for convenience.

Look for result symlinks

If you use nix-build, but not --no-build-output, your file system will be filled with result symlinks to various derivations. In the example above, note the following symlinks: 

/home/danbst/stack/new/website/server/result -> /nix/store/1jhmp6vl364p32r8bjigk65qh1xa562f-server-0.1.0.0
/home/ec2-user/result -> /nix/store/q35aq2sh5dbyka6g6f6qb7b8msxwds5m-nixos-system-iron-16.03.1299.a8e0739
/root/forkstat/result -> /nix/store/i5glmg3wk2a48x52rhd92zip1cmc0kq9-forkstat-git

How much space do these (apparently) abandoned derivations use? 

$ du -sch $(nix-store -qR /root/forkstat/result /home/ec2-user/result /home/danbst/stack/new/website/server/result)
...
3.4G    total

Not all of the derivations are garbage in this case, but quite a few are: 

# rm /root/forkstat/result /home/ec2-user/result /home/danbst/stack/new/website/server/result
# nix-collect-garbage -d
...
690 store paths deleted, 1817.99 MiB freed

Look for system derivations in particular. Those are created on many occasions, for example when running nixos-rebuild build-vm

Removing old generations

NixOS keeps old configurations of your system around so that you can always rollback to a previous configuration if something goes wrong. You can also select which generation to boot into via GRUB.

However these previous generations are GC roots that can keep around old, unnecessary software in your nix store. You can check what system generations you have with 

$ sudo nix-env -p /nix/var/nix/profiles/system --list-generations
...
  58   2021-09-04 02:56:54
  59   2021-09-05 07:12:43
  60   2021-09-05 22:12:13   (current)

You can remove all but the current generation with 

$ sudo nix-collect-garbage -d
...
4394 store paths deleted, 3467.28 MiB freed

There are also user-specific generations for different things (eg. home-manager). These can be removed with 

$ nix-collect-garbage -d

Reboot

As you see, the reference in /run/booted-system is a GC root, so it won't be cleared until reboot. If you don't want to reboot, just rm /run/booted-system that link and rerun sudo nix-collect-garbage.

Pinning

Running the following command: 

$ nix-instantiate shell.nix --indirect --add-root ./.nix-gc-roots/shell.drv ...

Will create a persistent snapshot of your shell.nix dependencies, which then won't be garbage collected, as long as you have configured keep-outputs = true (and haven't changed the default of keep-derivations = true). This is useful if your project has a dependency with no substitutes available, or you don't want to spend time waiting to re-download your dependencies every time you enter the shell.

You need to re-run that nix-instantiate command any time your shell.nix changes.

And there is a subtle gotcha if your shell.nix happens to evaluate to more than one derivation: nix-instantiate will number each derivation sequentially, so if you change your shell.nix to contain fewer derivations, such that (for example) the name of the last GC root starts with shell.drv-7, then shell.drv-{8,9,10,11,12...} will be dangling and unused.

The easiest way to get around this is to delete the ./.nix-gc-roots directory periodically (i.e., any time you re-run the nix-instantiate command).

Don't forget to periodically check your GC roots, and remove any that you no longer need.

Automation

Garbage collection can be automated,[cf. 4] for example: 

configuration.nix

nix.gc = {
  automatic = true;
  dates = "weekly";
  options = "--delete-older-than 30d";
};

If using nix-darwin, use this to run on 0th day of every week: 

configuration.nix

nix.gc = {
  automatic = true;
  interval = { Weekday = 0; Hour = 0; Minute = 0; };
  options = "--delete-older-than 30d";
};

This can result in redownloads (tarballs fetched with import (builtins.fetchTarball ...) for example are not referenced anywhere and removed on GC), but it frees you from runnning GC manually.

It is also possible to automatically run garbage collection whenever there is not enough space left.[cf. 5] For example, to free up to 1GiB whenever there is less than 100MiB left: 

nix.extraOptions = ''
  min-free = ${toString (100 * 1024 * 1024)}
  max-free = ${toString (1024 * 1024 * 1024)}
'';

This is particularly useful when the store is on its own partition, see below.

Moving the store

/nix can reside on another device, which is useful if your root device is very small, and you have another, larger drive available.

If the new partition is on the same device, some benefit can be gained by formatting the partition on which nix resides with a different file system. For example: on a Raspberry Pi, f2fs could be used for a gain in I/O throughput.

Regardless of /nix's filesystem, it can also be mounted with noatime (as seen in the example below). This will reduce metadata writes, improving I/O and the device's lifespan.

This is easiest to set up while installing NixOS, but /nix can be moved on a live system:

All commands below are executed with root privileges

  1. Create a new partition
  2. Mount this new partition over /mnt 
    # mount -o defaults,noatime /dev/disk/by-label/nix /mnt/nix
  3. Copy everything from /nix to /mnt Trailing slashes are important, in that without them, rsync will create an additional directory of the same name at the destination. 
    # rsync --archive --hard-links --acls --one-file-system --verbose /nix/{store,var} /mnt/nix
  4. Mount the new partition as the new /nix 
    # umount /mnt/nix
# mount /dev/disk/by-label/nix /nix
  5. Restart nix-daemon 
    $ systemctl stop nix-daemon.service
$ systemctl restart nix-daemon.socket
$ systemctl start nix-daemon.service
  6. Add the new /nix partition to your /etc/nixos/configuration.nix 
    {
   # ...
   fileSystems."/nix" = {
     device = "/dev/disk/by-label/nix";
     fsType = "ext4";
     neededForBoot = true;
     options = [ "noatime" ];
   };
}
  7. Apply your configuration 
    # nixos-rebuild switch
  8. Reboot to be sure /nix/store is properly mounted

Optionally

  1. After reboot, check that /nix is mounted over your partition 
    # mount | grep "/nix" && echo "Nix store is on a new partition" || echo "Nix is on the old partition"
  2. Once you are sure everything works, you can delete the old store 
    # mkdir /tmp/old_root
# mount --bind / /tmp/old_root
# rm --recursive /tmp/old_root/nix
# umount /tmp/old_root
# rmdir /tmp/old_root

See also

  1. ↑ Nix Manual, 11. Garbage Collection
  2. ↑ nix-collect-garbage(1)
  3. ↑ nix-store(1), under OPERATION --GC
  4. ↑ nix.gc
  5. ↑ min-free and max-free
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